I have heard all of the following:
1. It makes the car unstable.
2. The sunroof will crack if you corner hard due to body roll.
3. The added weight of the 17" wheels + sunroof put the matrix into another class (SUV), so they had to in order to stay in the desired class.
4. They are limited on the supply of 17" wheels....so they chose to not offer both knowing they would have production issues.
I would tend to MAYBE believe #2 & 3....HOWEVER. The local dealership where I got my XR has sold two XRS w/ sunroof and the 18" TRD wheels + springs. Also, my salesman said that I could "void my warranty" by putting 17's on my car, however the mechanic said thats a load of crap and they have NO warnings from Toyota or TRD about larger wheels.
I would get the wheels. If you crack the sunroof...then put the 16's back on when you get warranty work done. I would also put some sort of springs on it just in case its a stability issue, should resolve that. A good strut brace would cut down on body roll as well.....
All theoretical knowledge...I am not saying I proved any of this, just observations (lies! lies I tell you!!).
Cheers.